Starting phenix.real_space_refine on Thu Mar 13 07:04:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuq_43536/03_2025/8vuq_43536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuq_43536/03_2025/8vuq_43536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vuq_43536/03_2025/8vuq_43536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuq_43536/03_2025/8vuq_43536.map" model { file = "/net/cci-nas-00/data/ceres_data/8vuq_43536/03_2025/8vuq_43536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuq_43536/03_2025/8vuq_43536.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5500 2.51 5 N 1492 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2789 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2697 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "G" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1554 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.03, per 1000 atoms: 0.81 Number of scatterers: 8657 At special positions: 0 Unit cell: (107, 113.848, 124.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1629 8.00 N 1492 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 149 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 24.9% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.570A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.937A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.554A pdb=" N PHE A 102 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.506A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.797A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.518A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.659A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.502A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.757A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.832A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.095A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.613A pdb=" N SER B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.933A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 4.312A pdb=" N GLN B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.675A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.672A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.872A pdb=" N VAL B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 196 through 198 No H-bonds generated for 'chain 'G' and resid 196 through 198' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.768A pdb=" N ASN I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 removed outlier: 3.751A pdb=" N ALA I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.749A pdb=" N HIS I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.502A pdb=" N LEU A 33 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.734A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.731A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.734A pdb=" N ASN A 341 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 344 " --> pdb=" O ASN A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 72 removed outlier: 7.047A pdb=" N ALA B 37 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.878A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.572A pdb=" N VAL B 341 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 348 " --> pdb=" O VAL B 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.857A pdb=" N LEU G 81 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 60 removed outlier: 3.551A pdb=" N GLY G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 97 " --> pdb=" O HIS G 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 190 " --> pdb=" O HIS G 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 186 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 159 through 163 Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.762A pdb=" N VAL I 10 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN I 39 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR I 90 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20 removed outlier: 4.072A pdb=" N VAL I 18 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 78 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 66 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 173 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 155 removed outlier: 4.065A pdb=" N TRP I 148 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS I 149 " --> pdb=" O SER I 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER I 192 " --> pdb=" O LYS I 149 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2801 1.34 - 1.46: 2083 1.46 - 1.58: 3917 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 8863 Sorted by residual: bond pdb=" CB PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 1.506 1.587 -0.081 3.90e-02 6.57e+02 4.28e+00 bond pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.70e-02 3.46e+03 3.80e+00 bond pdb=" CG PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.18e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CA ASN I 53 " pdb=" CB ASN I 53 " ideal model delta sigma weight residual 1.539 1.598 -0.058 4.88e-02 4.20e+02 1.43e+00 ... (remaining 8858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12010 2.82 - 5.64: 74 5.64 - 8.47: 8 8.47 - 11.29: 1 11.29 - 14.11: 1 Bond angle restraints: 12094 Sorted by residual: angle pdb=" CA PRO G 156 " pdb=" N PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 111.50 97.39 14.11 1.40e+00 5.10e-01 1.02e+02 angle pdb=" C THR I 83 " pdb=" CA THR I 83 " pdb=" CB THR I 83 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N PRO G 156 " pdb=" CD PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 103.80 98.76 5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" CA THR I 83 " pdb=" C THR I 83 " pdb=" N GLU I 84 " ideal model delta sigma weight residual 119.52 116.77 2.75 7.90e-01 1.60e+00 1.21e+01 angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 107.37 4.63 1.40e+00 5.10e-01 1.09e+01 ... (remaining 12089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4498 17.96 - 35.91: 566 35.91 - 53.87: 147 53.87 - 71.82: 24 71.82 - 89.78: 12 Dihedral angle restraints: 5247 sinusoidal: 1891 harmonic: 3356 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP I 138 " pdb=" CB ASP I 138 " pdb=" CG ASP I 138 " pdb=" OD1 ASP I 138 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 802 0.029 - 0.058: 393 0.058 - 0.087: 105 0.087 - 0.117: 82 0.117 - 0.146: 15 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB THR G 91 " pdb=" CA THR G 91 " pdb=" OG1 THR G 91 " pdb=" CG2 THR G 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 227 " pdb=" N ILE B 227 " pdb=" C ILE B 227 " pdb=" CB ILE B 227 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA VAL G 40 " pdb=" N VAL G 40 " pdb=" C VAL G 40 " pdb=" CB VAL G 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1394 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 155 " -0.089 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO G 156 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO G 156 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO G 156 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " -0.045 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 304 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 319 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 245 2.69 - 3.24: 8282 3.24 - 3.79: 12495 3.79 - 4.35: 15199 4.35 - 4.90: 26229 Nonbonded interactions: 62450 Sorted by model distance: nonbonded pdb=" O ASN I 53 " pdb=" ND2 ASN I 53 " model vdw 2.133 3.120 nonbonded pdb=" O MET I 3 " pdb=" OG SER I 25 " model vdw 2.146 3.040 nonbonded pdb=" O PHE B 195 " pdb=" N GLY B 197 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 93 " pdb=" OE2 GLU A 277 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN B 154 " pdb=" OG SER B 259 " model vdw 2.216 3.040 ... (remaining 62445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.790 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8863 Z= 0.184 Angle : 0.616 14.112 12094 Z= 0.328 Chirality : 0.042 0.146 1397 Planarity : 0.005 0.124 1541 Dihedral : 17.334 89.781 3071 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.06 % Favored : 87.51 % Rotamer: Outliers : 0.66 % Allowed : 35.83 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 1153 helix: 0.75 (0.37), residues: 218 sheet: -1.03 (0.32), residues: 317 loop : -1.89 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 284 HIS 0.005 0.001 HIS B 332 PHE 0.009 0.001 PHE B 210 TYR 0.021 0.001 TYR B 321 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 132 average time/residue: 0.2521 time to fit residues: 46.5818 Evaluate side-chains 127 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113663 restraints weight = 15627.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111019 restraints weight = 15621.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112518 restraints weight = 16012.291| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.180 Angle : 0.591 7.916 12094 Z= 0.309 Chirality : 0.043 0.138 1397 Planarity : 0.004 0.077 1541 Dihedral : 4.134 22.203 1244 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.62 % Favored : 87.94 % Rotamer: Outliers : 5.73 % Allowed : 29.00 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1153 helix: 0.88 (0.35), residues: 246 sheet: -0.80 (0.32), residues: 316 loop : -2.09 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS B 332 PHE 0.012 0.001 PHE B 210 TYR 0.012 0.001 TYR B 321 ARG 0.003 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8121 (ptm160) REVERT: A 162 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6909 (m90) REVERT: A 295 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8924 (tp) REVERT: G 49 SER cc_start: 0.8899 (p) cc_final: 0.8430 (m) REVERT: G 180 GLN cc_start: 0.5849 (pm20) cc_final: 0.3692 (tm-30) REVERT: I 53 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7960 (p0) outliers start: 52 outliers final: 29 residues processed: 174 average time/residue: 0.2525 time to fit residues: 60.8433 Evaluate side-chains 155 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 0.0070 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114519 restraints weight = 15912.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111760 restraints weight = 16010.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113204 restraints weight = 16444.331| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8863 Z= 0.156 Angle : 0.566 7.594 12094 Z= 0.292 Chirality : 0.042 0.143 1397 Planarity : 0.004 0.066 1541 Dihedral : 4.040 23.154 1241 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.58 % Favored : 88.99 % Rotamer: Outliers : 5.62 % Allowed : 29.44 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.26), residues: 1153 helix: 0.91 (0.35), residues: 249 sheet: -0.91 (0.32), residues: 310 loop : -2.00 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 332 PHE 0.016 0.001 PHE A 152 TYR 0.012 0.001 TYR B 321 ARG 0.003 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8117 (ptm160) REVERT: B 206 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7789 (pp) REVERT: B 207 ASP cc_start: 0.8323 (p0) cc_final: 0.7961 (p0) REVERT: B 348 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8821 (pp) REVERT: B 378 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7693 (t60) REVERT: G 49 SER cc_start: 0.9012 (p) cc_final: 0.8499 (m) outliers start: 51 outliers final: 31 residues processed: 169 average time/residue: 0.2018 time to fit residues: 48.1501 Evaluate side-chains 158 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110885 restraints weight = 15843.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109106 restraints weight = 15541.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109939 restraints weight = 17221.894| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8863 Z= 0.265 Angle : 0.605 7.805 12094 Z= 0.312 Chirality : 0.044 0.197 1397 Planarity : 0.004 0.060 1541 Dihedral : 4.299 22.873 1241 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.62 % Favored : 85.95 % Rotamer: Outliers : 7.50 % Allowed : 28.22 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.26), residues: 1153 helix: 0.71 (0.34), residues: 247 sheet: -0.94 (0.31), residues: 323 loop : -2.05 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 148 HIS 0.009 0.001 HIS A 293 PHE 0.016 0.001 PHE A 152 TYR 0.023 0.002 TYR B 180 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8161 (ptm160) REVERT: B 206 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7872 (pp) REVERT: B 207 ASP cc_start: 0.8287 (p0) cc_final: 0.7975 (p0) REVERT: B 348 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 378 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.7870 (t60) REVERT: G 180 GLN cc_start: 0.5573 (mp10) cc_final: 0.3221 (tm-30) REVERT: I 53 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7992 (p0) outliers start: 68 outliers final: 49 residues processed: 182 average time/residue: 0.1998 time to fit residues: 50.6439 Evaluate side-chains 178 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 44 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112400 restraints weight = 15779.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109641 restraints weight = 15764.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110639 restraints weight = 17037.148| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.194 Angle : 0.585 7.358 12094 Z= 0.298 Chirality : 0.043 0.149 1397 Planarity : 0.004 0.058 1541 Dihedral : 4.221 22.174 1241 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.71 % Favored : 87.86 % Rotamer: Outliers : 6.62 % Allowed : 29.11 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.26), residues: 1153 helix: 0.86 (0.34), residues: 247 sheet: -1.01 (0.31), residues: 323 loop : -2.02 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 148 HIS 0.005 0.001 HIS A 293 PHE 0.013 0.001 PHE A 152 TYR 0.016 0.001 TYR G 105 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8193 (ptm160) REVERT: B 206 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7883 (pp) REVERT: B 207 ASP cc_start: 0.8413 (p0) cc_final: 0.8081 (p0) REVERT: B 348 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 378 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.7850 (t60) REVERT: I 53 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7971 (p0) outliers start: 60 outliers final: 46 residues processed: 177 average time/residue: 0.1933 time to fit residues: 48.2502 Evaluate side-chains 179 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 134 CYS Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 111 GLN I 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110189 restraints weight = 15753.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107825 restraints weight = 14681.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108984 restraints weight = 15739.079| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8863 Z= 0.232 Angle : 0.602 7.784 12094 Z= 0.306 Chirality : 0.043 0.144 1397 Planarity : 0.004 0.053 1541 Dihedral : 4.283 22.291 1241 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.44 % Favored : 86.12 % Rotamer: Outliers : 7.28 % Allowed : 28.89 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1153 helix: 0.77 (0.34), residues: 247 sheet: -1.12 (0.30), residues: 330 loop : -2.00 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.007 0.001 HIS A 293 PHE 0.027 0.001 PHE B 186 TYR 0.018 0.001 TYR B 180 ARG 0.005 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 130 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8199 (ptm160) REVERT: B 206 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7910 (pp) REVERT: B 207 ASP cc_start: 0.8484 (p0) cc_final: 0.8172 (p0) REVERT: B 348 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 378 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7892 (t60) REVERT: I 53 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (p0) outliers start: 66 outliers final: 56 residues processed: 180 average time/residue: 0.1940 time to fit residues: 49.1088 Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 124 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 111 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111739 restraints weight = 15696.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109989 restraints weight = 14986.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110940 restraints weight = 14470.735| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8863 Z= 0.180 Angle : 0.593 7.784 12094 Z= 0.299 Chirality : 0.043 0.143 1397 Planarity : 0.004 0.051 1541 Dihedral : 4.254 21.544 1241 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.97 % Favored : 87.60 % Rotamer: Outliers : 6.84 % Allowed : 29.33 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 1153 helix: 0.96 (0.34), residues: 244 sheet: -1.05 (0.31), residues: 315 loop : -1.92 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 148 HIS 0.005 0.001 HIS A 293 PHE 0.011 0.001 PHE A 152 TYR 0.012 0.001 TYR B 321 ARG 0.005 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8271 (ptm160) REVERT: B 206 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7824 (pp) REVERT: B 207 ASP cc_start: 0.8432 (p0) cc_final: 0.8120 (p0) REVERT: B 348 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 378 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.7786 (t60) REVERT: G 154 TYR cc_start: 0.5806 (p90) cc_final: 0.5358 (p90) REVERT: I 53 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8057 (p0) outliers start: 62 outliers final: 49 residues processed: 174 average time/residue: 0.1901 time to fit residues: 47.0111 Evaluate side-chains 180 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.0170 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 chunk 94 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114003 restraints weight = 15864.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111443 restraints weight = 15200.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112859 restraints weight = 15392.882| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8863 Z= 0.161 Angle : 0.587 8.233 12094 Z= 0.296 Chirality : 0.042 0.143 1397 Planarity : 0.004 0.050 1541 Dihedral : 4.163 21.941 1241 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.19 % Favored : 88.29 % Rotamer: Outliers : 6.28 % Allowed : 30.32 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 1153 helix: 1.12 (0.35), residues: 245 sheet: -1.05 (0.31), residues: 312 loop : -1.94 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS G 173 PHE 0.010 0.001 PHE A 152 TYR 0.020 0.001 TYR B 180 ARG 0.005 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8299 (ptm160) REVERT: B 206 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7749 (pp) REVERT: B 207 ASP cc_start: 0.8416 (p0) cc_final: 0.8130 (p0) REVERT: B 348 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8738 (pp) REVERT: B 378 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7704 (t60) REVERT: G 154 TYR cc_start: 0.5741 (p90) cc_final: 0.5272 (p90) REVERT: I 53 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7974 (p0) outliers start: 57 outliers final: 42 residues processed: 173 average time/residue: 0.1840 time to fit residues: 45.2382 Evaluate side-chains 175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110819 restraints weight = 15917.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108768 restraints weight = 14759.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109614 restraints weight = 14943.935| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8863 Z= 0.238 Angle : 0.621 7.857 12094 Z= 0.314 Chirality : 0.045 0.450 1397 Planarity : 0.004 0.048 1541 Dihedral : 4.271 21.708 1241 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.32 % Favored : 87.16 % Rotamer: Outliers : 6.28 % Allowed : 30.54 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.26), residues: 1153 helix: 0.97 (0.34), residues: 245 sheet: -1.18 (0.30), residues: 326 loop : -1.90 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.003 0.001 HIS G 173 PHE 0.022 0.001 PHE B 186 TYR 0.017 0.001 TYR G 105 ARG 0.007 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 128 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8169 (ptm160) REVERT: A 153 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 206 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 207 ASP cc_start: 0.8456 (p0) cc_final: 0.8138 (p0) REVERT: B 348 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8732 (pp) REVERT: B 378 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.7819 (t60) REVERT: G 19 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8614 (mtp180) REVERT: G 154 TYR cc_start: 0.5743 (p90) cc_final: 0.5225 (p90) REVERT: I 53 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7885 (p0) outliers start: 57 outliers final: 47 residues processed: 172 average time/residue: 0.1880 time to fit residues: 45.5579 Evaluate side-chains 179 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 40.0000 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 chunk 9 optimal weight: 0.0070 chunk 7 optimal weight: 0.8980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 119 HIS I 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113148 restraints weight = 15802.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111619 restraints weight = 14397.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112684 restraints weight = 14418.829| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8863 Z= 0.164 Angle : 0.601 8.221 12094 Z= 0.301 Chirality : 0.044 0.426 1397 Planarity : 0.004 0.049 1541 Dihedral : 4.172 21.011 1241 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.58 % Favored : 88.90 % Rotamer: Outliers : 5.18 % Allowed : 32.19 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.26), residues: 1153 helix: 1.07 (0.34), residues: 245 sheet: -1.07 (0.31), residues: 316 loop : -1.88 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 284 HIS 0.003 0.001 HIS G 173 PHE 0.007 0.001 PHE G 68 TYR 0.021 0.001 TYR I 140 ARG 0.007 0.000 ARG G 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8297 (ptm160) REVERT: A 153 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 206 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7747 (pp) REVERT: B 207 ASP cc_start: 0.8348 (p0) cc_final: 0.8018 (p0) REVERT: B 348 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8763 (pp) REVERT: B 378 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7731 (t60) REVERT: I 51 ASP cc_start: 0.8528 (t0) cc_final: 0.8317 (t0) REVERT: I 53 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7903 (p0) outliers start: 47 outliers final: 39 residues processed: 166 average time/residue: 0.1892 time to fit residues: 44.5383 Evaluate side-chains 169 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.0040 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 119 HIS B 340 ASN I 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114296 restraints weight = 15761.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112640 restraints weight = 15350.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113819 restraints weight = 14723.147| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8863 Z= 0.168 Angle : 0.604 8.112 12094 Z= 0.303 Chirality : 0.044 0.411 1397 Planarity : 0.004 0.048 1541 Dihedral : 4.135 22.369 1241 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.84 % Favored : 88.64 % Rotamer: Outliers : 5.73 % Allowed : 32.19 % Favored : 62.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.26), residues: 1153 helix: 1.10 (0.35), residues: 245 sheet: -1.04 (0.31), residues: 312 loop : -1.90 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 284 HIS 0.003 0.000 HIS G 173 PHE 0.007 0.001 PHE B 210 TYR 0.013 0.001 TYR B 321 ARG 0.007 0.000 ARG G 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3353.39 seconds wall clock time: 60 minutes 55.06 seconds (3655.06 seconds total)